Hexane isomers play a vital role as feedstocks and fuel additives in the petrochemical industry. However, their similar physical and chemical properties lead to significant challenges in the separation process. Traditional thermal separation techniques are energy-intensive and lead to significant carbon footprint penalties. As such, there is a growing demand for the development of less energy-intensive nonthermal separation methods. Adsorption-based separation methods, such as using solid sorbents or membranes, have emerged as promising alternatives to distillation. Here, we report the successful synthesis of two novel metal-organic frameworks (MOFs), NU-2004 and NU-2005, by incorporating a carborane-based three-dimensional (3D) linker and using aluminum and vanadium nodes, respectively. These MOFs exhibit exceptional thermal stability and structural rigidity compared to other MIL-53 analogues, which is further corroborated using synchrotron studies. Furthermore, the inclusion of the quasi-spherical 3D linker in NU-2004 demonstrates significant advancements in the separation of hexane isomers compared to other MIL MOFs containing two-dimensional (2D) and aliphatic 3D linkers.